ArticleBMC bioinformatics2013
Exploring cavity dynamics in biomolecular systems.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT.Computational biology and chemistry · 2022Article
- A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation.BMC bioinformatics · 2020Article
- An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel.Molecules (Basel, Switzerland) · 2018Article
- Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.Scientific reports · 2018Article
- Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A Survey.Computer graphics forum : journal of the European Association for Computer Graphics · 2017Article
- Interactive exploration of ligand transportation through protein tunnels.BMC bioinformatics · 2017Article
- Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking.BMC bioinformatics · 2016Article
- Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.The Journal of membrane biology · 2015Review
- CHEXVIS: a tool for molecular channel extraction and visualization.BMC bioinformatics · 2015Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe internal cavities of proteins are dynamic structures and their dynamics may be associated with conformational changes which are required for the functioning of the protein. In order to study the dynamics of these internal protein cavities, appropriate tools are required that allow rapid identification of the cavities as well as assessment of their time-dependent structures.
resultsIn this paper, we present such a tool and give results that illustrate the applicability for the analysis of molecular dynamics trajectories. Our algorithm consists of a pre-processing step where the structure of the cavity is computed from the Voronoi diagram of the van der Waals spheres based on coordinate sets from the molecular dynamics trajectory. The pre-processing step is followed by an interactive stage, where the user can compute, select and visualize the dynamic cavities. Importantly, the tool we discuss here allows the user to analyze the time-dependent changes of the components of the cavity structure. An overview of the cavity dynamics is derived by rendering the dynamic cavities in a single image that gives the cavity surface colored according to its time-dependent dynamics.
conclusionThe Voronoi-based approach used here enables the user to perform accurate computations of the geometry of the internal cavities in biomolecules. For the first time, it is possible to compute dynamic molecular paths that have a user-defined minimum constriction size. To illustrate the usefulness of the tool for understanding protein dynamics, we probe the dynamic structure of internal cavities in the bacteriorhodopsin proton pump.
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